The long-term goal of this project is to facilitate rational design of polymer based gene delivery systems by providing microscopic understanding of the actions of polycations during the delivery process. The project will investigate a few critical issues raised by recent experimental developments that shed new understanding on the delivery process. These experimental studies suggest that polycations used in successful vector preparations may be divided into two different portions that play distinct roles during the delivery. First, as has been long established, a portion of the polycation interacts with the plasmid DNA, resulting in DNA condensation. Recent evidence has indicated that the amount of polycation needed for complete DNA condensation may be governed by simple charge neutralization principles and is independent of the molecular weight and branching structure of polycations. Second, successful vector preparations include an additional portion of polycations that remain free in solution. These 'excess' polycations may function to destabilize cell, endosome, and even nuclear membranes, aiding in release of the DNA from the endosome and importation into the nucleus. Although a complete clarification of the suggested delivery mechanism requires more experimental investigations, theoretical/computational investigations that examine these potential actions using multi-scale modeling techniques will be very helpful at this time. The current study will focus on polyethyleneimine (PEI), one of the most promising polymeric vectors that has recently made it to phase II clinical trials for treating HIV diseases and bladder carcinoma. PEI is commercially available in both linear and branched forms with a wide range of molecular weights. The proposed computational/theoretical studies will first develop coarse-grained models for PEI that reproduce their structures and properties in aqueous solution. Atomistic and derived coarse grained models will be used to investigate condensation of nucleic acids and destabilization of lipid membranes by PEI with different branching and molecular weights. The proposed computational studies will provide microscopic knowledge on the structures of the underlying systems and enable the establishment of the structure function relationship for PEI based gene delivery vectors.